alkaline lysis - (Sep/23/2008 )
After I centrifuge the product from alkaline lysis, i can see a lot of debris floating. I am wondering what will happen if i take the floating debris to next step( for example phenol chloroform extraction)
you will have more work to do as all that floating debris will end up on the phenol/aqueous interphase.
pellet will also be harder to resuspend compared to a cleaner pellet if you dry the pellet too much.
aside from that there is no harm. You could pour the supernatant into a new tube and spin that down again to remove all the floating debris. (Saves on the phenol, boss will be happy) It depends on how much junk is floating around.